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Unexpected cross-species contamination in genome sequencing projects

The raw data from a genome sequencing project sometimes contains DNA from contaminating organisms, which may be introduced during sample collection or sequence preparation. In some instances, these contaminants remain in the sequence even after assembly and deposition of the genome into public datab...

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Published in:	PeerJ (San Francisco, CA) CA), 2014-11, Vol.2, p.e675-e675
Main Authors:	Merchant, Samier, Wood, Derrick E, Salzberg, Steven L
Format:	Article
Language:	English
Subjects:	Analysis Anopheles Bacteria Bioinformatics Biology Bos taurus Cattle Chromosomes Computational Biology Computer science Contaminants Contamination Deoxyribonucleic acid DNA DNA sequencing Experiments Genome assembly Genomes Genomics Microbiology Microbiome Neisseria gonorrhoeae Nucleotide sequence Organisms Sequence analysis Sheep Software Studies
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description	The raw data from a genome sequencing project sometimes contains DNA from contaminating organisms, which may be introduced during sample collection or sequence preparation. In some instances, these contaminants remain in the sequence even after assembly and deposition of the genome into public databases. As a result, searches of these databases may yield erroneous and confusing results. We used efficient microbiome analysis software to scan the draft assembly of domestic cow, Bos taurus, and identify 173 small contigs that appeared to derive from microbial contaminants. In the course of verifying these findings, we discovered that one genome, Neisseria gonorrhoeae TCDC-NG08107, although putatively a complete genome, contained multiple sequences that actually derived from the cow and sheep genomes. Our findings illustrate the need to carefully validate findings of anomalous DNA that rely on comparisons to either draft or finished genomes.
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subjects	Analysis Anopheles Bacteria Bioinformatics Biology Bos taurus Cattle Chromosomes Computational Biology Computer science Contaminants Contamination Deoxyribonucleic acid DNA DNA sequencing Experiments Genome assembly Genomes Genomics Microbiology Microbiome Neisseria gonorrhoeae Nucleotide sequence Organisms Sequence analysis Sheep Software Studies
title	Unexpected cross-species contamination in genome sequencing projects
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